A Calibration Routine for Efficient ETD in Large-Scale Proteomics

被引：42
作者：
Rose, Christopher M. [1 ,3 ]
Rush, Matthew J. P. [1 ,3 ]
Riley, Nicholas M. [1 ,3 ]
Merrill, Anna E. [1 ,3 ]
Kwiecien, Nicholas W. [1 ,3 ]
Holden, Dustin D. [4 ]
Mullen, Christopher [4 ]
Westphall, Michael S. [3 ]
Coon, Joshua J. [1 ,2 ,3 ]
机构：
[1] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA
[2] Univ Wisconsin, Dept Biomol Chem, Madison, WI 53706 USA
[3] Univ Wisconsin, Genome Ctr Wisconsin, Madison, WI 53706 USA
[4] Thermo Fisher Sci, San Jose, CA USA
来源：
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY | 2015年 / 26卷 / 11期
关键词：
ETD; Ion/ion; Kinetics; Proteomics; Mass spectrometry; Calibration; Orbitrap; ELECTRON-TRANSFER DISSOCIATION; QUADRUPOLE ION-TRAP; TRANSFER ION/ION REACTIONS; PROTEIN-SEQUENCE ANALYSIS; MASS-SPECTROMETRY; PEPTIDE IDENTIFICATION; MONOCLONAL-ANTIBODIES; SEARCH ALGORITHM; DOWN ANALYSIS; PROTON;
D O I：
10.1007/s13361-015-1183-1
中图分类号：
Q5 [生物化学];
学科分类号：
071010 ; 081704 ;
摘要：
Electron transfer dissociation (ETD) has been broadly adopted and is now available on a variety of commercial mass spectrometers. Unlike collisional activation techniques, optimal performance of ETD requires considerable user knowledge and input. ETD reaction duration is one key parameter that can greatly influence spectral quality and overall experiment outcome. We describe a calibration routine that determines the correct number of reagent anions necessary to reach a defined ETD reaction rate. Implementation of this automated calibration routine on two hybrid Orbitrap platforms illustrate considerable advantages, namely, increased product ion yield with concomitant reduction in scan rates netting up to 75% more unique peptide identifications in a shotgun experiment.
引用
收藏
页码：1848 / 1857
页数：10
相关论文
共 69 条
  • [1] Instant spectral assignment for advanced decision tree-driven mass spectrometry
    Bailey, Derek J.
    Rose, Christopher M.
    McAlister, Graeme C.
    Brumbaugh, Justin
    Yu, Pengzhi
    Wenger, Craig D.
    Westphall, Michael S.
    Thomson, James A.
    Coon, Joshua J.
    [J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2012, 109 (22) : 8411 - 8416
  • [2] Statistical Analysis of Peptide Electron Transfer Dissociation Fragmentation Mass Spectrometry
    Chalkley, R. J.
    Medzihradszky, K. F.
    Lynn, A. J.
    Baker, P. R.
    Burlingame, A. L.
    [J]. ANALYTICAL CHEMISTRY, 2010, 82 (02) : 579 - 584
  • [3] Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry
    Chi, An
    Huttenhower, Curtis
    Geer, Lewis Y.
    Coon, Joshua J.
    Syka, John E. P.
    Bai, Dina L.
    Shabanowitz, Jeffrey
    Burke, Daniel J.
    Troyanskaya, Olga G.
    Hunt, Donald F.
    [J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2007, 104 (07) : 2193 - 2198
  • [4] Optimization of Electron Transfer Dissociation via Informed Selection of Reagents and Operating Parameters
    Compton, Philip D.
    Strukl, Joseph V.
    Bai, Dina L.
    Shabanowitz, Jeffrey
    Hunt, Donald F.
    [J]. ANALYTICAL CHEMISTRY, 2012, 84 (03) : 1781 - 1785
  • [5] Protein identification using sequential ion/ion reactions and tandem mass spectrometry
    Coon, JJ
    Ueberheide, B
    Syka, JEP
    Dryhurst, DD
    Ausio, J
    Shabanowitz, J
    Hunt, DF
    [J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2005, 102 (27) : 9463 - 9468
  • [6] Anion dependence in the partitioning between proton and electron transfer in ion/ion reactions
    Coon, JJ
    Syka, JEP
    Schwartz, JC
    Shabanowitz, J
    Hunt, DF
    [J]. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY, 2004, 236 (1-3) : 33 - 42
  • [7] Collisions or Electrons? Protein Sequence Analysis in the 21st Century
    Coon, Joshua J.
    [J]. ANALYTICAL CHEMISTRY, 2009, 81 (09) : 3208 - 3215
  • [8] Mass spectrometric analysis, automated identification and complete annotation of O-linked glycopeptides
    Darula, Zsuzsa
    Chalkley, Robert J.
    Baker, Peter
    Burlingame, Alma L.
    Medzihradszky, Katalin F.
    [J]. EUROPEAN JOURNAL OF MASS SPECTROMETRY, 2010, 16 (03) : 421 - 428
  • [9] Front-End Electron Transfer Dissociation: A New Ionization Source
    Earley, Lee
    Anderson, Lissa C.
    Bai, Dina L.
    Mullen, Christopher
    Syka, John E. P.
    English, A. Michelle
    Dunyach, Jean-Jacques
    Stafford, George C., Jr.
    Shabanowitz, Jeffrey
    Hunt, Donald F.
    Compton, Philip D.
    [J]. ANALYTICAL CHEMISTRY, 2013, 85 (17) : 8385 - 8390
  • [10] Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry
    Elias, Joshua E.
    Gygi, Steven P.
    [J]. NATURE METHODS, 2007, 4 (03) : 207 - 214
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